


Twisting Biology

by DRAMAticalNinja



Category: Naruto
Genre: Alpha Uchiha Sasuke, Alpha/Beta/Omega Dynamics, Bottom Uzumaki Naruto, Kidnapping, M/M, Mating Cycles/In Heat, Omega Uzumaki Naruto, Omegas are rare, Other Additional Tags to Be Added, Possessive Behavior, Threats of Rape/Non-Con, Top Uchiha Sasuke
Language: English
Status: In-Progress
Published: 2015-08-17
Updated: 2015-08-27
Packaged: 2018-04-15 05:34:30
Rating: Mature
Warnings: Rape/Non-Con
Chapters: 2
Words: 3,727
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/4594758
Author URL: https://archiveofourown.org/users/DRAMAticalNinja/pseuds/DRAMAticalNinja
Summary: <blockquote class="userstuff">
              <p>Naruto isn't as stupid as he lets everyone believe. In truth, Naruto is actually rather smart. He has to be or else people will find out his precious secret.</p><p>Believe it or not, Naruto is an omega. Not just any omega either, he is a pure, male omega; a second gender which is such a rarity that people question their very existence.</p>
            </blockquote>





	1. Prologue

**Author's Note:**

> So I'm usually not a big fan of stories which take away form the original plot line and never usually write them but this idea got stuck in my head and I couldn't resist!  
> The prologue is just a round up on how Naruto survived up to the Tenchi Bridge reconnaissance mission arc of the anime which is were the story picks up in chapter one. There will be a few spoilers of that arc but then the story will generally not be canon from that point.  
> Updates may be fairly slow like with my other stories but I'll try to hurry them up!:)  
> I don't have a beta so I apologise in advance for any mistakes or errors!  
> Thank you for reading<3  
> ~DN

** ~Prologue~ **

** Successful Hiding **

 

When everyone looked at Naruto, they all looked at him with hate and anger in their eyes, connecting him as the source of their losses in the past. They walked the opposite direction when they saw him, whispering cruel words to their companions and dragging their children away with a tight grip. All throughout his childhood, people never bothered with Naruto. They kept their fixed opinions of him.

_'Oh, that's the stupid nine tails brat! Such an evil child!'_

_'Keep away from him, who knows what he's capable of.'_

Now then, Naruto might be the holder of the nine tails but he was in no way evil, anyone who actually gets to know him can see his pure heart. Another inaccurate fact the villagers have never bothered to correct is that Naruto isn't as stupid as he lets everyone believe. In truth, Naruto is actually rather smart. He has to be or else people will find out his precious secret.

Believe it or not, Naruto is an omega. Not just any omega either, he is a pure, male omega; a second gender which is such a rarity that people question their very existence. Less than 6% of the known population are omegas and less than 2% are male. The majority of people never even meet an omega in their lifetime and the ones that do rarely let them leave their sights again, bonding them - by force if necessary - and keeping their omega hidden and out of harm from others. The temptation of an omega has been told to be so strong, it makes your skin itch below the surface from the moment you encounter their sweet scent. Feuds have took place just to decide who gets to own a precious omega and even wars have begun over the rare male omega. 

The academy gives lessons to their students on second gender biology at the age of 9, a year before they discover their dynamic. These lessons are compulsory for all ninjas and ninjas-in-training, even those who have already graduated must take these sessions. It’s well known Naruto doesn’t always listen in his classes but one thing caught his attention during his first session.

‘An _omega, as rare as they are, cannot be taken on as a ninja of the village.’_

Ever since then, for a whole year, Naruto felt uneasy and wary, something kept gnawing at the back of his mind. It wasn’t normal. As he found out on the day of his tenth birthday thanks to the burning heat coursing his body and the indescribable and confusing want which flooded his mind, he was an omega and in his first heat. It was awful, despite the lessons briefly going over an omega heat, Naruto was completely unprepared, scared and alone. The scent and state of his apartment managed to down his scent for the heat (assisted by drowning his body in the shower) which thankfully only lasted a half a day. During that time, Naruto mind drifted to the signs he should have noticed; his small, slight form compared to all his classmates and his fair, almost feminine, features. He should have guessed since those lessons but couldn’t comprehend it.

Afterwards, all Naruto felt was rage. How could he become Hokage if he couldn’t be a ninja due to his _damn dynamic_? It wasn’t fair, he should be able to graduate just like everybody else! His second gender shouldn’t define him, he didn’t want to be constantly on the run from alpha suitors or stuck in some room all day for ‘protection’ or used as some breeding machine. No, that life was not for Naruto, he was going to become Hokage even if it killed him!

It was at this point that Naruto decided that no one must know his true second gender, he would pose as an average beta if anyone would ask. Thankfully his birthday had landed on the long weekend in remembrance of the nine tails attack so he had a few days to prepare himself before returning to the academy. Blocking his scent, Naruto found, was fairly easy. There were a whole range of scent suppressor pills made for alpha ninjas going on missions and not wanting their overpowering scent to reveal them. Naruto actually had a bottle in his apartment, a shop keeper had thrown it at him when he’d wandered too close to their stall.

It worked surprisingly well, Naruto couldn’t even smell his sweet honey-like omega scent after two days of taking them (two in the morning and two at night). The only issue was the scent glandes on his neck; they let out a slight whiff of his scent after training he found whilst testing the theory in his apartment. To solve this issue, Naruto exchanged his regular black Konaha top for a bright orange, high collared jacket. He lined the collar with a neutral scent spray he picked up in the market whilst transformed as a plain civilian woman, also acting as a test just in case someone could smell him.

By the time it came to return to the academy, Naruto was nervous but confident he’d hidden his gender well. It was a bit difficult being at the academy, his class seemed to hold an extra-ordinary amount of alphas who just smelled delicious to Naruto. All his instincts were telling him to tilt his head and expose his neck to them, making it difficult to act normally. He didn’t want to submit to anyone, not for his gender, that wasn’t who he was!  Sitting in class, his eyes had bulged when Kiba sat next to him, causing him to freeze as he started sniffing the air around him in confusion. He only relaxed when he turned to Naruto with a smug grin and a “So, a beta, huh?” If he could trick an Inuzuka which their mighty noses, Naruto was sure he was home free.

After that first day, it was easy. No one questioned his gender or really cared. It got easier and easier to face and be level with the alphas and ignore his instincts. Everything was just like it usually was. He knew he’d have to find some way to stop his heats if he really wanted to pose as a beta for the rest of his life, what if a heat started whilst he was on a mission?  Omegas had two heats a year, one starting on their birthday and one directly six months after that. They grow in length each time until an omega is at the peck of their birthing prosperity then they start to decline again.

Naruto started to frequent the Konaha library in his spare time, once again disguised as another, to read up on anything he could to do with omega heats. It took some time, much to his worry as his second heat was slowly approaching, but the omega finally found a ruffled book revealing how an omega could prevent their heats. It was quite simple really, just a recipe to follow similar to creating food pills to be taken every five days. When his second heat came around, Naruto barricaded himself inside his apartment and praying to kami that it worked. It did, Naruto felt no effects of heat except his cheeks being slightly flushed.

Finally, Naruto felt secure and confident that he wouldn’t be found out. Not too confident though, he was still wary of over-training in the presence of others or being too tired around alphas and letting his instincts take over. Speaking up to and arguing with alphas got easier as the years past as well. He learnt to ignore their scents for the most part, some particularly strong alpha always made him have to hold back a whine. That damn Uchiha for example. He always seemed so brooding and angry, his scent reflected off that and was so strong to Naruto’s senses. It drives him crazy and causes him to stumble when they spar. He _hates_ it entirely and the alpha.

Other than that, Naruto successfully hidden his true gender for the next five and a half years. There were times he was sure he’d revealed himself, when Sasuke left his emotions were running so high he was almost certain the scent of a distressed omega would burst through his suppressors. But no one found out then and no one ever did except one.  The incident with Jiraiya-sensei whilst training was Naruto’s downfall. The four tails state had completely made him loose control and after it was over his skin was totally singed and burning away. It cancelled out and wore away the effect of the suppressors, allowing his natural honey and scent that was _oh so omega_ to be revealed, stronger than ever due to the pain and distress he was in.

Jiraiya struggled to believe that Naruto had managed to hide this from everyone and had to keep control of his inner alpha from bonding with the young man. Despite how utterly _delicious_ the omega smelt and how his skin itched at being close to an omega in distress, Jiraiya understood Naruto’s reasoning for keeping his secret and as much as it pained him to not bond after the truth was out, he continued to travel and train Naruto. His self-control was thankfully superb as he’d been lucky enough to meet another omega, not a male one however and they smell so much sweeter for some reason, before in his travels.

 After returning to the village and being sent to rescue Gaara, meeting more Akatsuki members along the way, Naruto was certain that no one else suspected him of being anything more than a beta. He had proven he could take care of himself and was powerful, so very unlike the stereotypical omega. He doubted that anyone would truly discover his second gender at this point, he’d managed to hide it so well in a village full of trackers and interrogators.

_What’s the worst that could happen?_

* * *

 

“Now I’ll explain our mission.

Our objective is to head towards the Tenchi Bridge in order to capture the Akatsuki spy working under Orochimaru.  

This is a rare chance for us to obtain information on Orochimaru and Uchiha Sasuke.”

Naruto’s eyes widened slightly.

_Sasuke_


	2. Chapter One

**Summary for the Chapter:**

> Naruto arrives at Tenchi Bridge, his emotions run wild.

**Notes for the Chapter:**

> Wow guys, I'm so shocked at the response the first chapter got!  
> I never expected to get so many kind comments:')  
> This chapter will have spoilers for the Tenchi Bridge mission arc then after this chapter and part of the next one the events of the story will, for the most part, move away from the actual plot of Naruto.  
> As usual, I have yet to get a beta (if anyone would be up to the job, please let me know:3) so all mistakes are my own and I apologise!  
> Thank you so much for reading!<3  
> ~DN

** ~Chapter One~ **

** Losing Control**

 

Naruto sighed pleasantly, walking slowly behind the others with his hands folded behind his head. Despite how annoyed he was about the newest member of Team Kakashi, that Sai person, Naruto couldn’t help but internally relax due to the lack of alpha presence. With Sakura being a beta and the two new members being… well, Naruto assumes they’re betas since they don’t have a scent. Who knows, they seem kind of weird. As much as Naruto respected and enjoyed being led by Kakashi-sensei, sometimes his alpha scent was so overpowering and made Naruto have to keep a tight leash on his instincts, so a mission without it was a pleasant change in his eyes.

_This mission_

Naruto closed his eyes and inhaled deeply to smooth himself. He knew he could never fully relax. They were finally going to get information on Sasuke; that means he was one step closer to bringing him home. After nearly three years, Naruto could feel himself getting closer to fulfilling his promise to Sakura. Naruto couldn’t explain his need to bring Sasuke home, they were always arguing before he left. But when Sasuke did leave, Naruto felt an ache in his chest which he couldn’t explain. Maybe his omegian instincts were working automatically, Sasuke was an alpha that was close to Naruto after all and to leave him so suddenly must have had a negative effect on him.

That should all change shortly though. Despite this being a just an intelligence research mission, Naruto could feel it in his bones that he would see Sasuke. They’d travelled this far, Naruto was sure he’d finally find Sasuke. Just the thought of Sasuke being in the hands of that creepy alpha for this long was enough to fuel his determination, why couldn’t he understand the snake was only using him? It made Naruto’s emotions run wild and he knew he’d have to keep a hold of his anger and bitterness throughout this mission. He couldn’t have his omega scent breaking through his suppressors now.

“There’s no presence of anyone around the Tenchi Bridge yet.”

Sai’s monotone voice brought Naruto out of his thoughts. His eyes snapped to the group in front of him. He’d been so involved with his thoughts about Sasuke that he hadn’t noticed everyone had stopped and Sai had apparently done a perimeter check. Looking around the group whilst Yamato made commands, Naruto’s breathing hitched as he took in the sight of the bridge.

This is it, this is where he’d find out about Sasuke. His skin tickled at the thought for some reason and he rubbed his hand over his neck unconsciously. _Strange_

 As Captain Yamato explained what was going to happen, Naruto found himself listening quietly and not giving much input. His mind was preoccupied, thinking about scenarios for if they saw Sasuke today. He'd convince him to come home no matter what it took, he'd never give up on his comrade. As Yamato continues his instructions, he gave Naruto a photograph to hold for him. He was shocked for a moment to see the Akatsuki member Sasori, before he remembered the task of this mission.

_Of course Yamato-sensei needed to see Sasori._

Naruto internally scolded himself for getting so side tracked with his thoughts about Sasuke. He would be no good in this mission if he kept getting distracted by the alpha. Working as hard as he had over the years, Naruto couldn't afford any screw ups with either his abilities or masking his second gender during this mission. Focusing his resolve as Yamato transformed into Sasori and tested his voice, Naruto pledged to concentrate fully on the mission, leaving his instincts under lock and key.

_Focus on the mission._

As Naruto, Sakura and Sai parted ways from the transformed Yamato, they made their way to a location where they could see the bridge. Following Saukra, who determined the wind would help mask the presence, they moved closer to the bridge, crouching behind a larger moss covered boulder. Naruto's skin started to inch with uneasiness for a reason unknown to him. It was nearly noon, the heat was rising in their stuffy hiding spot making the trio restless. Naruto broke the heavy silence first. 

He growled slightly, something Naruto rarely did as an omegas growl was lighter (thankfully in this situation it could be classed as him trying to be quiet), before he spoke, "That lousy spy, why isn't he showing up?"

The other two were silent for a few moments before Sai's small gasp broke the air.

"He's here."

Both Sakura and Naruto copied Sai's gasp before turning their attention back to the crucial bridge. A figure, whose form was completely covered by a blue robe, stood at the opposite side of the bridge. They seemed somewhat familiar to Naruto but as they held no prominent scent, due to them either being a beta or using suppressors, he couldn't place the person in his mind. He watched intently, breath held, as the figure moved across the bridge, stopping in the middle before looking off to one side. The trio could still not see the spy's face.

The tinkling of a bell informed them of Yamato’s steady approach. The cover of the Hiruko puppet travelled slowly across the bridge to meet up with the spy in the centre. Due to the wind, the trio could barely hear the conversation between the two on the bridge as they engaged each other. It made Naruto nervous and he gripped his jacket sleeve to calm himself.

The spy slowly turned his head and Naruto growled once more, his anger rising due to the figure. _Kabuto!_ Naruto clenched his teeth in anger to prevent any more growls, his hand grips the rock and threatened to crush it.

 It was fairly obvious that Naruto has a serious dislike for the beta but he knew he had to try control his anger, for fear of his scent getting revealed. It had never happened before, well, in public that was. There was this one time between missions when he was lazing at home for a few days and forgot his suppressors. Thankfully he got his scent covered again before he left for his next mission. He did get shouted at by Sakura though for not leaving his house, if only she knew the real reason why.

Naruto watched the interaction between Yamato and Kabuto with narrowed eyes, his anger a steady flow coursing through his body. Everything seemed to be going to plan but Naruto couldn’t shake a feeling he had, especially when Kabuto whipped around so determined as if expecting someone.

Then, it all happened suddenly. Naruto smelt him first. It was a scent he would never be able to forget as long as he lived. It was a putrid, vile scent of rotting carcasses yet it was undeniably alpha. Never had an alpha scent made Naruto want to vomit before, they’d made him want to whine and jump the owner but never vomit. It was disgusting, from years of messing with his body with experiments. Orochimaru appeared on the bridge just moments later, causing Kabuto to jump back to ‘Sasori’s’ side.

_That alpha_

Naruto could barely control his rage at the site of him. He took Sasuke away from him. _His_ Sasuke! The snake wanted to use him for his eyes and body, how dare he! Naruto could feel himself begin to shake as Kabuto turned on Yamato, ruining his disguise. Both of them here is too much for Naruto to bare as the pair joined forces against Yamato.

Naruto continues shaking in silent fury as he can feel his teeth elongating. He knows his eyes must be red by now and his features must have turned more animalistic. _Damn it!_ Naruto tries to regain himself but it’s no use, the sight of these two have left him in a state of pure, unresolved anger.

Naruto’s eyes widen as Yamato gives the signal and he trio leap into action, landing on the bridge before their temporary leader. They were now so close to the snake duo and Naruto recognised they were speaking to them but couldn’t process the words in his fury. That is until, the snake voiced the name on his mind for so long.

“…Sasuke.”

Naruto sees red, he emits short violent growls and his features become even more animalistic. His figure is hunched over and still shaking, his sharpened fingernails ripping into the bridge.

**_“Give Sasuke back! You give him back!”_ **

Naruto voice is deep and shaken when he speaks, a dangerous aura being emitted from his person. All thoughts of withholding his anger gone the moment he landed on the bridge.

The last thing he notices is the widening of his enemy’s eyes as the nine tailed cloak covers his form before darkness.

 

* * *

 

 

 _“_ _…’s that delightful sce…”_

_“…Naruto’s a…”_

_“…how…impossible…”_

Naruto can here faint voices as he teeters on the edge of consciousness. His skin feels like it has been set ablaze and his skull feels crushed. His body is aching entirely.

_What happened?_

Wincing but unable to open his eyes, Naruto tries to recall what happened. He remembers the mission, it going downhill, landing on the bridge then… nothing at all. His burning body is making it hard for Naruto to think.

_I haven’t felt like this since that time with Jiraiya…Oh please - no!_

Naruto’s eyes snap open in realisation. He must’ve gone into four tails mode again! But that means… his scent…

Naruto cautiously turns his head, wincing as he does, to look at the people crouched by his form.

_Sakura_

_Yamato-sensei_

Naruto could already smell his unique honey omega scent, they surely knew his secret by now. He closed his eyes in aching defeat. He worked so hard to prevent this moment from happening, six years of effort just gone in a moment.

“Naruto”

Sakura’s timid and barely recognisable voice entered his conscious and he opened his eyes to face her. The first thing he noticed was her larger than usual pupils and the slight occasional twitch in her hands, both of which he knew was due to his scent. Despite being a beta, it would still affect Sakura. Glancing to her left, he saw Yamato was faring much better and showed no signs of being affected.

“H-how… W-why did you never say anything?” Reverting his attention back to Sakura, he noticed her voice was unsteady and she had unshed tears in her eyes. She looked like she was struggling to restrain himself and moved to inch forward before Yamato place his hand on her shoulder.

Naruto sighed before replying. “I didn’t wanted to be treated like I was fragile or couldn’t do anything. I want to be hokage, it’s my dream.” Naruto’s voice begins to crack at the end.

He would never be able to achieve that dream now. Surely when they got back to village he would be under strict supervision and mated off as soon as possible, perhaps even to multiple people. People would be fighting for his attention but keeping him under locks. He might never see sunlight again, might even be kept in chains for his ‘safety’. Naruto shivered at the thought, tears welling up in his eyes. He wouldn’t let them fall though, he was stronger than that.

“Oh Naruto,” Sakura started but Naruto’s mind was elsewhere.

Screw his dynamic, Naruto would finish this mission and find Sasuke. He’d never let it stop him before so why now? If he was going to be locked up when he got back, the least he could do in his final mission was bring Sasuke home, he had to.

With new determination, Naruto interrupted Sakura causing her to gasp. Omegas aren’t meant to able to do that or so she thought. She seemed to forget that Naruto was an omega before this day and wouldn’t change just because they found out.

“Enough, Sakura.” Naruto sits up and begins getting to his feet with determination resting surely in his eyes.

“Come on, let’s go find Sasuke!”

**Notes for the Chapter:**

> Please comment, I would love to hear your feedback!:3

**Author's Note:**

> Please comment, I would love to hear your feedback!:3


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